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MolNFT v1 · #51873 · protein

Site-directed mutagenesis of the catalytic tryptophan environment in pleurotus eryngii versatile peroxidase

2VKA · Versatile peroxidase VPL2: “Site-directed mutagenesis of the catalytic tryptophan environment in pleurotus eryngii versatile peroxidase”. X-ray diffraction, 3 ligands (HEM, CA, SO4), 1 pocket (best druggability 0.80). MolNFT v1…

PDB
2VKA
Type
protein
Length
317 residues
Chains
1
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Versatile peroxidase VPL2
EC
1.11.1.16
UniProt
O94753
Ligands
HEM, CA, SO4
Pockets
1 · best druggability 0.80

Structure

x-ray diffraction · 1 distinct chain · 42% helix, 6% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
AVersatile peroxidase VPL2 (EC 1.11.1.16)protein31742% helix, 6% strandO94753

Ligands and binding sites

  • HEM · Protoporphyrin IX containing Fe · ligand · chains A
  • CA · Calcium ion · metal · 2 copies · chains A
  • SO4 · Sulfate ion · ion · chains A
  • GOL · Glycerol · additive · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
13880.800.8944HEM

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

  • 2VKA · Site-Directed Mutagenesis of the Catalytic Tryptophan Environment in Pleurotus eryngii… · the same entry in another collection · chain A against A, TM-score 1.00
  • O94753 · AlphaFold monomer V2.0 prediction for versatile peroxidase VPL2 (O94753) · a predicted model of the same protein · chain A against A, TM-score 0.99

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